barnlarv

This is a companion R package to the paper:

Wong, J. Y., Chan, K. Y. K., & Chan, B. K. K. (2018). Phylogenetic, ecological and biomechanical constraints on larval form: A comparative morphological analysis of barnacle nauplii. PLoS ONE, 13(11): e0206973. doi:10.1371/journal.pone.0206973

Findings reported in the paper can be reproduced with the datasets and codes from this package.

NEW: Interactive version of the figures

Easier way to explore the data and understand the analysis. CLICK HERE to view the interactive plots.

plotly.mp4

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Installation:

• using tarball from releases page*. In R:

install.packages("<path to downloaded zip/tarball>",repos = NULL)

• using devtools. In R:

devtools::install_github("jinyung/barnlarv")

*Note:

1. binaries for Windows not provided, devtools method should work across platforms.

2. releases page also contains package manual.

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Using data from the package

Outlines and sampled outlines dataset

Interspecific barnacle nauplii outline and sampled outline datasets can be found in data directory and called directly in R, e.g.:

data(stage2outline)
data(stage2landmark)

see ?outline or ?semilandmark for help files of these datasets. These datasets were pre-processed from raw images stored in inst/extdata/stage2/larvae_drawing and inst/extdata/ontogeny/larvae/drawing directories. The processing can be reproduced following the codes stored in data-raw directory. In data-raw, the .tps files of the sampled outlines are also available and can be imported into other geometric morphometrics software.

Covariates and phylogeny data

Data for covariates used in the main analyses can be found here or called in R with:

read.csv(system.file("extdata/stage2", "frontal-horn-summary.csv",
         package = "barnlarv"))

Data of phylogeny for a subset of species can be found here or called in R with:

ape::read.tree(system.file("extdata/perez-tree-37-species", 
               package = "barnlarv"))

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Reproducing the results

All tables and figures can be reproduced following the dynamic R markdown documents, which can be download here.

There are three files inside .zip:

1. figures_and_tables.Rmd
2. supplementary_figures_and_tables.Rmd
3. preamble.tex

file 1 will produce figures and tables in the main paper; file 2 will produce the supplementary tables and figures; file 3 is used for formatting in knitr compilation of Rmd files for pdf outputs. Compiling the Rmd files will reproduce the results*.

*NOTE: the figures, tables, and supplements were created with barnlarv v0.0.2, as such can only be 100% reproduced with the specific R session environment used when the paper was written. See v0.0.2 release notes for details.